[BioC] Problems using text to subset array information from an expression set

[Jeff Lande]

Kasper,

On traceback(), I just get

> traceback()
1: newdata["1007_s_at", ]

One thing that I noticed when trying to compare expression sets that I was
able to use text for subscripting and those that I was not was that the
se.exprs was a <0 x 0 matrix> for the former and NA for the latter.  

Also, there is a UNIX version that I use for processing large data sets and
a PC version that I use for less memory intensive work (I have control of
updating packages, etc with the PC version but I don't have administrative
rights on the UNIX version).  I used a workaround to subset by arrays.  When
I assigned a new phenoData object to the subset (within the PC version), I
was able to use text subscripting on the resulting expression set (code
below).  

> atsarrays <- c("AA1.CEL, ..., "AA132.CEL")
> atsmatch <- sampleNames(alldata) %in% atsarrays
> atsdata <- alldata[,atsmatch]
> pd <- read.phenoData("ATS_phenodata.TXT")
> phenoData(atsdata) <- pd
> atsdata <- new('exprSet', exprs=exprs(atsdata), phenoData = pd)
>

I'm still confused why I was having trouble using text to subscript, but I
seem to be able to continue on with analysis now.

Thanks,

Jeff

Jeff: you are using a very old version of Biobase (1.5.12). If I use  
a current version (1.8.0) I can subset exprSet's in the way you want  
(tested by running the example for exprSet and then subsetting using
  eset["31738_at",]
)

It might also (instead of just being an old version) be because of  
the way the exprSet is constructed using rma. Could you do the following
   1) Do a traceback() after the error
   2) test what the rownames/colnames are of
exprs(Data), se.exprs(Data)
I assume that se.exprs(Data) is a <0 x 0 matrix>.

/Kasper

On Apr 4, 2006, at 11:31 AM, Benilton Carvalho wrote:

> isn't
>
>   exprs(alldata)["1007_s_at",]
>   exprs(alldata)[, "AA100.CEL"]
>
> what you want?
>
> b
>
> On Tue, 4 Apr 2006, Jeff Lande wrote:
>
>> I have an odd problem that I cannot seem to figure out.
>>
>> I have a set of CEL files in a directory, which I read using the  
>> ReadAffy()
>> command.  Then I run the rma command to preprocess.
>>
>>> Data <- ReadAffy()
>>> alldata <- rma(Data)
>>
>> I've done this many times before without problems.  However, when  
>> I try to
>> use text instead of numbers for subscripting, I get an error.
>>
>> For example, I am able to access data from the first row and  
>> column using
>> numeric subscripts
>>
>>> alldata[1,1]
>> Expression Set (exprSet) with
>>        1 genes
>>        1 samples
>>                 phenoData object with 1 variables and 1 cases
>>         varLabels
>>                sample: arbitrary numbering
>>
>> but using text for either subscript, I get an error.
>>
>>> alldata["1007_s_at",]
>> Error in alldata["1007_s_at", ] : no 'dimnames' attribute for array
>>> alldata[,"AA100.CEL"]
>> Error in alldata[, "AA100.CEL"] : no 'dimnames' attribute for array
>>
>> I actually went through what I think was the same process last  
>> week (and
>> many times previously) and had no problems, so I'm stumped.
>>
>> Here is my session information:
>>
>>> sessionInfo()
>> R version 2.1.0, 2005-04-18, ia64-unknown-linux-gnu
>>
>> attached base packages:
>> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices"  
>> "utils"
>> [7] "datasets"  "base"
>>
>> other attached packages:
>> hgu133acdf       affy reposTools    Biobase
>>   "1.4.3"    "1.6.7"   "1.5.19"   "1.5.12"
>>
>> I must be missing something obvious, but I just can't figure out  
>> what is
>> going wrong.  Does anyone have insight into this problem?
>>
>> Jeff Lande
>> Post-Doctoral Associate
>> University of Minnesota
>>
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>
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